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Galkin S, Rozina A, Zalevsky A, Gottikh M, Anisenko A. A Fluorescent Assay to Search for Inhibitors of HIV-1 Integrase Interactions with Human Ku70 Protein, and Its Application for Characterization of Oligonucleotide Inhibitors. Biomolecules 2020; 10:E1236. [PMID: 32854330 PMCID: PMC7563236 DOI: 10.3390/biom10091236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/21/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
The search for compounds that can inhibit the interaction of certain viral proteins with their cellular partners is a promising trend in the development of antiviral drugs. We have previously shown that binding of HIV-1 integrase with human Ku70 protein is essential for viral replication. Here, we present a novel, cheap, and fast assay to search for inhibitors of these proteins' binding based on the usage of genetically encoded fluorescent tags linked to both integrase and Ku70. Using this approach, we have elucidated structure-activity relationships for a set of oligonucleotide conjugates with eosin and shown that their inhibitory activity is primarily achieved through interactions between the conjugate nucleic bases and integrase. Molecular modeling of HIV-1 integrase in complex with the conjugates suggests that they can shield E212/L213 residues in integrase, which are crucial for its efficient binding to Ku70, in a length-dependent manner. Using the developed system, we have found the 11-mer phosphorothioate bearing 3'-end eosin-Y to be the most efficient inhibitor among the tested conjugates.
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Affiliation(s)
- Simon Galkin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (A.R.); (A.Z.)
| | - Anna Rozina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (A.R.); (A.Z.)
| | - Arthur Zalevsky
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (A.R.); (A.Z.)
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russia
| | - Marina Gottikh
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Andrey Anisenko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia; (S.G.); (A.R.); (A.Z.)
- Chemistry Department, Lomonosov Moscow State University, 119992 Moscow, Russia;
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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Characterization of HIV-1 integrase interaction with human Ku70 protein and initial implications for drug targeting. Sci Rep 2017; 7:5649. [PMID: 28717247 PMCID: PMC5514147 DOI: 10.1038/s41598-017-05659-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 06/01/2017] [Indexed: 11/27/2022] Open
Abstract
Human Ku70/Ku80 protein is known to influence HIV-1 replication. One of the possible reasons may be the protection of integrase from proteasomal degradation by Ku70 subunit. We demonstrated that recombinant HIV-1 integrase and Ku70 form a stable complex, while no interaction of Ku70 with integrase from prototype foamy virus was observed. By analyzing protein subdomains we determined two binding sites in the structure of both Ku70 and integrase: the 51–160 a.a. region of integrase interacts with residues 251–438 of Ku70, whereas Ku70 N-terminal domain (1–250 a.a.) contacts an α6-helix in the 200–220 a.a. integrase region. Single substitutions within integrase (E212A or L213A) block the interaction with Ku70 thus indicating that the binding site formed by the 200–220 a.a. integrase region is crucial for complex formation. E212A/L213A substitutions decreased the integrase capacity to bind Ku70 in HEK293T cells. A conjugate of 2′-ОMe-GGUUUUUGUGU oligonucleotide with eosin is shown by molecular modeling to shield integrase residues E212/L213 and is effective in blocking complex formation of Ku70 with integrase what makes the complex between α6-helix and Ku70(1–250) a possible target for drug development.
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Korolev SP, Zatsepin TS, Gottikh MB. Oligonucleotide inhibitors of HIV-1 integrase efficiently inhibit HIV-1 reverse transcriptase. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Specific features of HIV-1 integrase inhibition by bisphosphonate derivatives. Eur J Med Chem 2014; 73:73-82. [DOI: 10.1016/j.ejmech.2013.11.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/24/2013] [Accepted: 11/27/2013] [Indexed: 12/31/2022]
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Billamboz M, Suchaud V, Bailly F, Lion C, Demeulemeester J, Calmels C, Andréola ML, Christ F, Debyser Z, Cotelle P. 4-Substituted 2-Hydroxyisoquinoline-1,3(2H,4H)-diones as a Novel Class of HIV-1 Integrase Inhibitors. ACS Med Chem Lett 2013; 4:606-11. [PMID: 24900718 DOI: 10.1021/ml400009t] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/17/2013] [Indexed: 12/25/2022] Open
Abstract
A series of 2-hydroxy-1,3-dioxoisoquinoline-4-carboxamides featuring an N-hydroxyimide chelating functionality was evaluated for their inhibitory properties against human immunodeficiency virus type 1 integrase (HIV-1 IN). Several derivatives displayed low nanomolar IC50 values comparable to that of the clinically used raltegravir. A marked effect of one compound on both primary IN-catalyzed reactions, strand transfer (ST), and 3' processing (3'-P), emphasizes a novel IN inhibition mechanism establishing it as a potential new generation IN inhibitor. Substitution of the 2-hydroxyisoquinoline-1,3-dione scaffold at position 4 by carboxamido chains was beneficial for antiviral activity since reproducible low micromolar anti-HIV activities were obtained for the first time within this scaffold.
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Affiliation(s)
- Muriel Billamboz
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Virginie Suchaud
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Fabrice Bailly
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Cedric Lion
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
| | - Jonas Demeulemeester
- KU Leuven, Molecular Virology and Gene Therapy (VCTB+5), Kapucijnenvoer 33,
B-3000 Leuven, Flanders, Belgium
| | - Christina Calmels
- UMR 5234 CNRS, Université Bordeaux Segalen, 146 Rue Léo Saignat, F-33076 Bordeaux, France
| | - Marie-Line Andréola
- UMR 5234 CNRS, Université Bordeaux Segalen, 146 Rue Léo Saignat, F-33076 Bordeaux, France
| | - Frauke Christ
- KU Leuven, Molecular Virology and Gene Therapy (VCTB+5), Kapucijnenvoer 33,
B-3000 Leuven, Flanders, Belgium
| | - Zeger Debyser
- KU Leuven, Molecular Virology and Gene Therapy (VCTB+5), Kapucijnenvoer 33,
B-3000 Leuven, Flanders, Belgium
| | - Philippe Cotelle
- Université Lille Nord de France, F-59000 Lille, France
- Université Lille 1 Sciences & Technologies, EA 4478 Chimie Moléculaire et Formulation, F-59655 Villeneuve d’Ascq, France
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